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CBOL Working Groups

CBOL Working Groups. David E. Schindel, Executive Secretary National Museum of Natural History Smithsonian Institution SchindelD@si.edu ; http://www.barcoding.si.edu 202/633-0812; fax 202/633-2938. CBOL’s Working Groups. Database: Designing/constructing the BARCODE data standards

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CBOL Working Groups

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  1. CBOL Working Groups David E. Schindel, Executive Secretary National Museum of Natural History Smithsonian Institution SchindelD@si.edu; http://www.barcoding.si.edu 202/633-0812; fax 202/633-2938 South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007

  2. CBOL’s Working Groups • Database: Designing/constructing the BARCODE data standards • DNA: Protocols for formalin-fixed and old museum specimens; Producing LIMS for dissemination • Data Analysis: Beyond phenetic methods; population genetics perspective • Plants: Identify gene region(s) for barcoding

  3. BARCODE Data Standards • Consensus results of Front Royal meeting • GBIF  ITIS  GRIN • NBII  Species2000  IPNI • ICZN  ZooRecord  OBIS • Structured link to voucher specimen • Species name selected from authority • Online access to metadata • Trace files and quality scores • Minimum sequence length

  4. BARCODE Records in INSDC Specimen Metadata Voucher Specimen Species Name GeoreferenceHabitatCharacter setsImagesBehaviorOther genes Indices - Catalog of Life - GBIF/ECAT Nomenclators - Zoo Record - IPNI - NameBank Publication links - New species Databases - Provisional sp. Barcode Sequence Trace files Primers Other Databases Literature(link to content or citation) PhylogeneticPop’n GeneticsEcological

  5. Digitizing Taxonomic Literature • CBOL’s catalytic efforts: • Library-Laboratory meeting in London, 2005, on electronic access to taxonomic literature • Led to formation of Biodiversity Heritage Library initiative • Industrial-scale digitization of pre-1923 taxonomic literature; free online access • OCR and Taxonomic Intelligence • Partner in Encyclopedia of Life informatics

  6. CBOL’s Working Groups • Database: Designing/constructing the BARCODE data standards • DNA: Protocols for formalin-fixed and old museum specimens; Producing LIMS for dissemination • Data Analysis: Beyond phenetic methods; population genetics perspective • Plants: Identify gene region(s) for barcoding

  7. CBOL Formalin Workshop • May 8-9, 2006 workshop in Washington, National Research Council • Literature survey of DNA recovery protocols from formalin-fixed specimens Chemists, biochemists, biophysicists, biomedical researchers • Create a new research agenda • Follow-on with SPNHC as major partner

  8. CBOL’s Working Groups • Database: Designing/constructing the BARCODE data standards • DNA: Protocols for formalin-fixed and old museum specimens; Producing LIMS for dissemination • Data Analysis: Beyond phenetic methods; population genetics perspective • Plants: Identify gene region(s) for barcoding

  9. CBOL’s Working Groups • Database: Designing/constructing the BARCODE data standards • DNA: Protocols for formalin-fixed and old museum specimens; Producing LIMS for dissemination • Data Analysis: Beyond phenetic methods; population genetics perspective • Plants: Identify gene region(s) for barcoding by December 2006

  10. Progress toward Plant Barcode • Kress 2005 proposal for ITS and trnh-psbA • Kew Garden receives Sloan/Moore Foundation support, early 2005 • Phase 1 screens 100 genes across 50 sibling species pairs • Phase 2 tests of matK, rpcoC1, rpoB, ndhJ, and accD • Canadian proposal for rbcL • CBOL protocols for approving barcode regions

  11. Wider Impacts of Barcoding • Catalyzing interoperability of databases • Barcode data standards link sequences, specimens, species names and publications • Improving information infrastructure • Digital library initiative in taxonomy • Expanding analytical toolbox for taxonomy • Renewing the mission of museums • DNA recovery from formalin-fixed specimens

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